Re: [ccp4bb] Validity of Ion Sites in PDB

Given the average resolution of protein structures, reliability of ion site identification is almost always in question. Realistically, I think that only a combination of approaches and evaluation of several factors (including other experimental methods) leads to good answers (as I am trying to

Re: [ccp4bb] Validity of Ion Sites in PDB

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jacob, the 'check-my-metal' server at http://csgid.org/csgid/metal_sites/ lists a couple of references which might be of interest. As usual in crytallography one must understand the science in order to understand the reliability of the models

Re: [ccp4bb] Validity of Ion Sites in PDB

Dear all, It is well known that you can look at anomalous difference maps to see heavier atoms - although I think not enough people do it. One technique that I think is powerful, but under-used is to calculate element-specific maps by taking the difference of anomalous difference data from

[ccp4bb] CCP4-6.4.0 Update 010

Dear CCP4 Users, An update for the CCP4-6.4.0 series has just been released, consisting of the following changes ◆ ARP/wARP (Mac, Linux) 1. Fix in the use of free R flag in the ARP/wARP CCP4i interface for solvent building 2. Fix in the identification of non-crystallographic symmetry that in

Re: [ccp4bb] CCP4 lib file

Thanks Eleanor, I ended up using a glucose ligand lib file from a different protein that my friend used and refinement Refmac5 worked out. However I need to add the LINK Command in PDB so CCP4 recognizes that glucoses connected. Can I get help please? Thank you, Remie On Mar 5, 2014, at

Re: [ccp4bb] CCP4 lib file

Have you run refmac with the Review restraints option - that generates LINKs if they seem necessary. Or can you use the SUGAR links already set upin the library? Eleanor On 7 March 2014 11:51, Remie remiefa...@gmail.com wrote: Thanks Eleanor, I ended up using a glucose ligand lib file from

Re: [ccp4bb] Validity of Ion Sites in PDB

There is another paper out there, which describes the use of long wavelengths to define anomalously scattering substructures. This method certainly helps to distinguish water molecules from something else, such as chloride for instance.

Re: [ccp4bb] CCP4 lib file

On 07/03/14 11:51, Remie wrote: I ended up using a glucose ligand lib file from a different protein that my friend used and refinement Refmac5 worked out. The mind boggles :)... well, OK. However I need to add the LINK Command in PDB so CCP4 recognizes that glucoses connected. In

[ccp4bb] docking program

Can anyone recommend a good docking program to look at protein-DNA interactions?

Re: [ccp4bb] CCP4-6.4.0 Update 010

Hi, Is the refmac5 indeed 5.8.006? The current ccp4 version 5.8.0049. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220Skype: boaz.shaanan Fax:

Re: [ccp4bb] Validity of Ion Sites in PDB

Dear Jacob, An example where special efforts were made to investigate biocatalysis and the role of ions, harnessing both softer X-rays and ion substitutions and a WASP analysis to be sure as possible of their identity, can be found here:- http://www.ncbi.nlm.nih.gov/pubmed/20099851 The review

Re: [ccp4bb] Validity of Ion Sites in PDB

Dear all and dear Jacob Please have also a look at another paper from Manfred where they show that both difference electron-density maps and anomalous difference electron-density maps suggest that in crystals grown from a sodium sulfate solution PPE binds Na+ in its metal-binding site.

Re: [ccp4bb] CCP4-6.4.0 Update 010

Hi Boaz It is 5.8.0069 And it prints the correct version for me on all platforms Andrey On 7 Mar 2014, at 13:13, Boaz Shaanan wrote: Hi, Is the refmac5 indeed 5.8.006? The current ccp4 version 5.8.0049. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the

Re: [ccp4bb] Validity of Ion Sites in PDB

You indicate that oxygen anomalous scattering could be used; whilst this is applicable to chirality determination in small molecule organic crystallography the oxygen anomalous signal is very small and to my knowledge not used thus far in protein crystallography. Perhaps I should have been

Re: [ccp4bb] CCP4-6.4.0 Update 010

Dear CCP4 Users as ever with life, a couple of errors have made it into the update a. ipmosflm.exe 7.1.0 is missing from the windows update b. a small change in ccp4i/src/imosflm means that MOSFLM_EXEC is not being set for csh users. The suggested remedy is for windows users to hold off this

[ccp4bb] POSTDOCTORAL POSITION AVAILABLE IN STRUCTURAL BIOLOGY

A postdoctoral position is available at the Laboratory of Structural Biology and Chemistry (www.icsn.cnrs-gif.fr/guittet) of the Institute of Chemistry of Natural Compounds (ICSN) in Gif-sur-Yvette, France, 20km southwest of Paris. The project aims at understanding the mechanisms of action of

Re: [ccp4bb] Validity of Ion Sites in PDB

Dear Jacob, Ah yes, I see. Your wording is perfectly clear. Sorry for my misunderstanding. Best wishes, John Prof John R Helliwell DSc On 7 Mar 2014, at 15:18, Keller, Jacob kell...@janelia.hhmi.org wrote: You indicate that oxygen anomalous scattering could be used; whilst this is

[ccp4bb] New Deadline for Athens Workshop on Strategic pipeline planning: from sample preparation to 3D structure determination with bio SAXS and other biophysical techniques

Dear colleagues, I am writing to inform you that the deadline for our workshop on *Strategic pipeline planning: from sample preparation to 3D structure determination with bio SAXS and other biophysical techniques *to be held at the National Hellenic Research Foundation (NHRF) in Athens from April

Re: [ccp4bb] density near Histidine

Dear SDY, It looks like ethylene glycol to me. Try EDO (http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-searchoperation=ccidtarget=EDO) Avinash -- Avinash S. Punekar Uppsala University